Methods in Ecology and Evolution

Article	Citations
	331
Cover Picture and Issue Information	210
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Cover Picture and Issue Information	134
Cover Picture and Issue Information	125
occupancyTuts : Occupancy modelling tutorials with RPresence	123
A network theoretic method for the basic reproductive number for infectious diseases	101
Individualised niches in a variable environment—Consequences for environmental change responses	98
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	95
FlywayNet : A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	84
Empirical dynamic programming for model‐free ecosystem‐based management	82
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	81
State‐space models and inference approaches for aquatic animal tracking with passive acoustic telemetry and biologging sensors	78
Filtering heart rates using data densities: The boxfilter R package	74
Using cloud radar to investigate the effect of rainfall on migratory insect flight	73
Incidence‐data‐based species richness estimation via a Beta‐Binomial model	63
AF‐vapeR : A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	60
Toward a unified approach to modelling adaptation among demographers and evolutionary ecologists	54
Inferring state‐dependent diversification rates using approximate Bayesian computation	53
ECOGEN : Bird sounds generation using deep learning	52
How to get the most out of phylogenetic imputation without abusing it	52
From anarchy to clarity, data pre‐processing and statistical choices influence quantitative environmental DNA ( eDNA	52
Individual tree extraction through 3D promptable segmentation networks	51

Exploring congruent diversification histories with flexibility and parsimony	50
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	48
Beneath the buzz: Quantifying nest locations and densities of ground‐nesting wild bees (Hymenoptera: Anthophila)	48
Nighthawk : Acoustic monitoring of nocturnal bird migration in the Americas	47
A new centrality index designed for multilayer networks	47
A pluralistic framework for measuring, interpreting and decomposing heterogeneity in meta‐analysis	46
BATScan: A radar classification tool reveals large‐scale bat migration patterns	46
Towards biologically realistic estimates of home range and spatial exposure for colonial animals	45
A systematic method for hypothesis synthesis and conceptual model development	42
Long‐term automated visual monitoring of Antarctic benthic fauna	42
Towards ‘digital ecology’: Advances in integrating artificial intelligence from data generation to ecological insight	41
The ecological forecast limit revisited: Potential, absolute and relative system predictability	41
An open future for MEE	41
Navigating through space and time: A methodological approach to quantify spatiotemporal connectivity using stream flow data as a case study	41
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks	39
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity	38
A 3D modelling approach to measuring structural characteristics of bird nest interiors	37
Classifying the activity states of small vertebrates using automated VHF telemetry	37
Integrated movement models for individual tracking and species distribution data	36
EcoEnsemble: A general framework for combining ecosystem models in R	36
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package	35
Data reconciliation in multi‐trait experiments with kinship ordination	35
A general framework for jointly modelling thermal and hydric constraints on developing eggs	34
lacunr: Efficient 3D lacunarity for voxelized LiDAR data from forested ecosystems	34
M oon S hine : A software‐hardware system for simulating moonlight ground illuminance and re‐creat	34
Multi‐trait point pattern reconstruction of plant ecosystems	33
Scalable semantic 3D mapping of coral reefs with deep learning	31
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Benchmarking imputation methods for categorical biological data	31
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Cover Picture and Issue Information	31
TinyCO 2 : High‐performance, low‐cost CO	29
qad : An R‐package to detect asymmetric and directed dependence in bivariate samples	29
Using standardized fish‐specific autonomous reef monitoring structures ( FARMS ) to quantify cryptobenthic fish communities	29
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves	29
When to monitor or control: Informed invasive species management using a partially observable Markov decision process ( POMDP ) framework	28
PleistoDist : A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos	28
Sourcing high tissue quality brains from deceased wild primates with known socio‐ecology	28
Measuring understorey vegetation structure using a novel mixed‐reality device	28
Retrodiction of forest demography: Backward simulation with reverse matrix models	28
Issues in calibrating models with multiple unbalanced constraints: the significance of systematic model and data errors	27
An aquaria set‐up for long‐term, multiple‐stressor research in marine organisms	27
Using causal diagrams and superpopulation models to correct geographic biases in biodiversity monitoring data	27
RFIDeep: Unfolding the potential of deep learning for radio‐frequency identification	27
The Benthic Underwater Microscope imaging PAM ( BUMP ): A non‐invasive tool for in situ assessment	27
Introducing recurrent event analyses to assess species interactions based on camera‐trap data: A comparison with time‐to‐first‐event approaches	27
The Wayqecha Amazon Cloud Curtain Ecosystem Experiment: A new experimental method to manipulate fog water inputs in terrestrial systems	27
PicoCam: High‐resolution 3D imaging of live animals and preserved specimens	26
Same data, different results? Machine learning approaches in bioacoustics	26
Trait coevolution and causal inference using generalized dynamic phylogenetic models	26

A global estimator of C and N isotope baselines for fresh waters	26
Detecting and reducing heterogeneity of error in acoustic classification	26
Microclimf: Fast modelling of microclimate across real landscapes in R	26
treats: A modular R package for simulating trees and traits	25
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species	25
A Double machine learning trend model for citizen science data	25
Existing and emerging uses of drones in restoration ecology	25
Handbook of protocols for standardized measurements of floral traits for pollinators in temperate communities	25
The power of forecasts to advance ecological theory	25
Sensors versus surveyors: Comparing passive acoustic monitoring, camera trapping and observer‐based monitoring for terrestrial mammals	25
Automated identification of diverse Neotropical pollen samples using convolutional neural networks	25
Correction to: Quantifying degradation in animal acoustic signals with the R package baRulho	25
Estimating process‐based model parameters from species distribution data using the evolutionary algorithm CMA‐ES	24
A process approach to quality management doubles NEON sensor data quality	24
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface	24
Cover Picture and Issue Information	24
OpenSoundscape: An open‐source bioacoustics analysis package for Python	23
The CV is dead, long live the CV !	23
Data‐driven discovery of mechanistic ecosystem models with LLMs	23
A wireless, remotely operable and easily customizable robotic flower system	23
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning	23
Paying attention to other animal detections improves camera trap classification models	23
Tracking the frequency of phytoplankton clonal lineages using multispectral image flow cytometry and neural networks	23
In situ estimation of active dispersal abilities in reef fish early life stages using tracking technologies	23
Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling	23
A short guide for effective field data collection	23
Vegetation patterns pinpoint the least resilient dryland sites	23
TreeCompR : Tree competition indices for inventory data and 3D point clouds	22
A terrestrial laser scanning‐based workflow for component‐wise estimation of individual tree above‐ground biomass	22
Synthesizing forecasts to inform decision‐making and advance ecological theory	22
Addressing spatial confounding in geostatistical regression models: An R‐ INLA approach	22
Design and performance of an ecosystem‐scale forest soil warming experiment with infrared heater arrays	22
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Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all	22
Cover Picture and Issue Information	22
Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on local extinctions for many Red List species	21
starve: An R package for spatio‐temporal analysis of research survey data using nearest‐neighbour Gaussian processes	21
Temporal design for aquatic organismal sampling across the National Ecological Observatory Network	21
Precise tactile stimulation of worker ants by a robotic manipulator reveals that individual responses are density‐ and context‐dependent	21
sound C lass : An automatic sound classification tool for biodiversity monitoring using machine learning	21
Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees	21
Towards scalable insect monitoring: Ultra‐lightweight CNNs as on‐device triggers for insect camera traps	20
ipsecr: An R package for awkward spatial capture–recapture data	20
COPIS : A robust and versatile robotic imaging system for the 3D digitization of natural history specimens with photog	20
Reconstructing Langevin systems from high‐ and low‐resolution time series using Euler and Hermite reconstructions	20
Animal geolocation with convolution algorithms in Julia and R via Wahoo.jl	20
Methods to account for incomplete viewsheds in distance sampling	20
NAPS : Integrating pose estimation and tag‐based tracking	20
DeepDiveR—A software for deep learning estimation of palaeodiversity from fossil occurrences	20
poolHelper : An R package to help in designing Pool‐Seq studies	20
Guidelines for the prediction of species interactions through binary classification	20
How to generate accurate continuous thermal regimes from sparse but regular temperature measurements	20
Impact of sampling strategy on inference of community assembly processes in phylogenetic island biogeography	20
Estimating interaction strengths for diverse horizontal systems using performance data	20
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	19
Monitoring fast‐moving animals—Building a customized camera system and evaluation toolset	19
Practical guidelines and the EMLN R package for handling ecological multilayer networks	19
sabinaNSDM : An R package for spatially nested hierarchical species distribution modelling	19
tidysdm : Leveraging the flexibility of tidymodels for species distribution modelling in R	19
soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes	19
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Estimating spatiotemporal reproductive dynamics of fish populations with passive acoustic monitoring: A state‐space model approach	18
A low‐cost IoT network to monitor microclimate variables in ecosystems	18
Long‐term collar deployment leads to bias in soil respiration measurements	18
Real‐time alerts from AI‐enabled camera traps using the Iridium satellite network: A case‐study in Gabon, Central Africa	18
Cover Picture and Issue Information	18
Correction to ‘An evaluation of multi‐species occupancy models with correlated species occurrences’	18
Quantifying the utilisation of blue, green and brown resources by riparian predators: A combined use of amino acid isotopes and fatty acids	18
A GLMM approach for combining multiple relative abundance surfaces	18
ecochange: An R‐package to derive ecosystem change indicators from freely available earth observation products	18
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Improved order selection method for hidden Markov models: A case study with movement data	18
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PiCAM : A Raspberry Pi‐based open‐source, low‐power camera system for monitoring plant phenology in Arctic environments	18
Pitfalls arising from site selection bias in population monitoring defy simple heuristics	18
Hard tissue thin‐sectioning techniques in vertebrate paleohistology: Review, synthesis and improvements	17
Non‐invasive reconstruction of complete mitochondrial genomes from aquatic environmental DNA using PCR‐free long‐read sequencing	17
A novel generalized spatial mark‐resight model that accounts for group associations	17
Including the invisible fraction in whole population studies: A guide to the genetic sampling of unhatched bird eggs	17
3D photogrammetry as a low‐cost and non‐invasive method for acoustic modelling of animal hearing	17

Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring	17
The persistent advantage of model‐based phylogenetic methods for single‐trait prediction	17
Correction to ‘The Aquatic Metatron: A large‐scale experimental facility to study the combined effects of habitat fragmentation and climate change on aquatic meta‐ecosystems’	17
Modelling approaches for meta‐analyses with dependent effect sizes in ecology and evolution: A simulation study	17
A framework for post‐processing bird tracks from automated tracking radar systems	17
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Applying the maximum entropy principle to neural networks enhances multi‐species distribution models	16
Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer	16
Streamlining analysis methods for large acoustic surveys using automatic detectors with operator validation	16
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Acoustic and archival technologies join forces: A combination tag	16
Studying collective animal behaviour with drones and computer vision	16
Rapid construction of insect–plant interaction networks via multiplexed long‐fragment DNA metabarcoding and NGS	16
Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data	16
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A conceptual framework for host‐associated microbiomes of hybrid organisms	16
Advancing aquatic biodiversity assessments of invertebrates using eDNA metabarcoding: A systematic evaluation of primers for marine and freshwater co	16
Extending isolation by resistance to predict genetic connectivity	16
Connectivity conservation planning through deep reinforcement learning	15
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ChirpArray : A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	15
TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	15
CATS : A high‐performance software framework for simulating plant migration in changing environments	15
Clustering and unconstrained ordination with Dirichlet process mixture models	15
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3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	15
Time‐lapse cameras bridge the gap between remote sensing and in situ observations of tundra phenology	15
Sap Flow Analyzer : A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	15
Quantifying macro‐evolutionary patterns of trait mean and variance with phylogenetic location–scale models	15
Correction to ‘ PhyBaSE : A Bayesian structural equation model approach to causal inference in phylogenetic comparative analyses’	15
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	15
Cover Picture and Issue Information	15
theRmalUAV: An R package to clean and correct thermal UAV data for accurate land surface temperatures	15
ENphylo : A new method to model the distribution of extremely rare species	15
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	14
Impact of acoustic index parameters on soundscape comparisons	14
Investigating soil mesofauna cryptic diversity: Current challenges and perspectives	14
Realising the promise of large data and complex models	14
Generating continuous maps of genetic diversity using moving windows	14
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	14
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	14
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	14
One number to rule them all: The Wildlife Sperm Index for standardized gamete assessment	14
PoolDilutionR : An R package for easy optimization of isotope pool dilution calculations	14
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	13
Estimating animal density for a community of species using information obtained only from camera‐traps	13
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	13
USE it: Uniformly sampling pseudo‐absences within the environmental space for applications in habitat suitability models	13
Mitigating pseudoreplication and bias in resource selection functions with autocorrelation‐informed weighting	13
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats	13
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HSC 3 D : A Python package to quantify three‐dimensional habitat structural complexity	13
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	13
AMMonitor 2: Remote monitoring of biodiversity in an adaptive framework in R	13
Robust passive sampling of airborne environmental DNA to monitor plants and animals	13
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	13
Systematic review and best practices for drone remote sensing of invasive plants	13
Ten practical guidelines for microclimate research in terrestrial ecosystems	13
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A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys	13
A new tool to improve the estimates of interaction rewiring considering the whole community composition	13
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates	13
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model	13
plantTracker : An R package to translate maps of plant occurrence into demographic data	12
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Bioregionalization analyses with the bioregion R package	12
Beyond the next step: A multi‐criteria generative validation framework for step selection functions	12
Avoiding confusion: Modelling image identification surveys with classification errors	12
High‐magnification platform for characterising microscopic communities	12
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	12
Simple assay quantifying sediment resuspension effects on marine carbon storage	12
Fine‐scale reconstruction of pelagic fish migration by iso‐logging of eye lens	12
Home‐range spillover in habitats with impassable boundaries: Causes, biases and corrections using autocorrelated kernel density estimation	12
metaRange : A framework to build mechanistic range models	12
A new method for voxel‐based modelling of three‐dimensional forest scenes with integration of terrestrial and airborne LiDAR data	12
mpmsim: An R package for simulating matrix population models	12
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models	12
Deep reinforcement learning for conservation decisions	12
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning	12
EEMtoolbox : A user‐friendly R package for flexible ensemble ecosystem modelling	12
An RGB‐D framework for capturing soft‐sediment microtopography	12
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patter: Particle algorithms for animal tracking in R and Julia	12
ohun: An R package for diagnosing and optimizing automatic sound event detection	12
Distinguishing passive and driven trait evolution in the presence of boundaries	12
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DImodelsMulti: An R package for fitting Diversity‐Interactions models to repeated measures or multivariate data	11
Resin‐coated urea effectively simulates the chronic dynamics of natural nitrogen deposition	11
Detecting stochasticity in population time series using a non‐parametric test of intrinsic predictability	11
Coupling gel electrophoresis with photoluminescence reveals biochrome complexes in modern and fossil shells	11
Spatially explicit management of genetic diversity using ancestry probability surfaces	11
The RadOrgMiner pipeline: Automated genotyping of organellar loci from RADseq data	11
Adaptive sampling in ecology: Key challenges and future opportunities	11
Ecoacoustics for context‐rich direct and indirect trophic interaction data and ecological network construction	11
STbayes : An R package for creating, fitting and understanding Bayesian models of social transmission	11